The bodies were brought to the hospital as the naval hospital INHS Ashvini does not have facilities to conduct autopsies.
Besides the autopsy to determine the causes of death, DNA samples have been taken and dental identification carried out to identify the victims.
Hospital officials said the bodies were brought in a completely charred state though some tissues were intact.
Orthopaedic x-rays carried out to ascertain shrapnel or other foreign bodies embedded on the victims have proved negative.
Prima facie, doctors have concluded death due to burning, asphyxiation and drowning thought the exact cause and timing of death of each will be determined only at a later stage.
The identities of the victims shall be clear after forensic experts give the DNA and dental record reports in the next few days.
Meanwhile, the Indian Navy is under pressure to expedite the work of recovering the remaining 13 missing sailors.
After five bodies were recovered till Friday evening, the naval team of divers is engaged in a round-the-clock operation to find the others.
The chances of finding any survivor have been ruled out from the deep sea fighter vessel which exploded, caught fire and then sank within six hours early Wednesday in the Mumbai naval harbour.
"The state of (the three recovered bodies) and conditions within the submarine leads to the firm conclusion that finding any surviving personnel within the submarine is unlikely," the Indian Navy said in a statement Friday afternoon.
"The damage and destruction within the submarine around the control room area indicates that the feasibility of locating bodies in the forward part of the submarine is also very remote as the explosion and very high temperatures, which melted steel within, would have incinerated the bodies too," the statement added.
However, the Indian Navy is hopeful that some of the armaments inside the deep sea fighter vessel, stored on the rear side, may be recovered undamaged as the flames did not completely gut that portion of the submarine.
The distraught families of all the 18 missing personnel have been contacted "and are being provided regular updates through constant interaction" by the Family Cell headed by a rear admiral and members of the Navy Wives Welfare Association.